Artifice is a webcomic found here: http://webcomics.yaoi911.com/archive/artifice-page-1/. It is complete at 88 pages, and author's notes clarify the ending and answer some other questions.
It is beautifully drawn and the story is gripping. However, the world it is set in is beyond grim - pretty much the definition of a Crapsack World (http://tvtropes.org/pmwiki/pmwiki.php/Main/CrapsackWorld)
The story begins with Deacon, an android soldier, on a mission with his brethren to kill a lot of people - apparently civilians who know too much. This is Deacon:
I say he is a soldier because he dresses and acts like one, but apparently he and his cohort are actually the property of a powerful corporation. Deacon runs into Jeff, who is an outcast among the (now dead) colonists because he is gay. This is Jeff:
These events are told through flashback, as Deacon is debriefed by the clever and ruthless Dr. Maven, who is trying to find out why the mission went so horribly wrong and what, if anything, is worth salvaging in the malfunctioning Deacon.
Jeff is a prisoner of the corporation, if he isn't already dead, and Dr. Maven has the codeword to control Deacon and is strongly hinting he will be scrapped as soon as she is done questioning him.